Affine Gap Research Articles

A Dibenzo[g,p]chrysene‐Based Organic Semiconductor with Small Exciton Binding Energy via Molecular Aggregation

AbstractExciton binding energy (Eb) is understood as the energy required to dissociate an exciton in free‐charge carriers, and is known to be an important parameter in determining the performance of organic opto‐electronic devices. However, the development of a molecular design to achieve a small level of Eb in the solid state continues to lag behind. Here, to investigate the relationship between aggregation and Eb, star‐shaped π‐conjugated compounds DBC‐RD and TPE‐RD were developed using dibenzo[g,p]chrysene (DBC) and tetraphenylethylene (TPE). Theoretical calculations and physical measurements in solution showed no apparent differences between DBC‐RD and TPE‐RD, indicating that these molecules possess similar properties on a single‐molecule level. By contrast, pristine films incorporating these molecules showed significantly different levels of electron affinity, ionization potential, and optical gap. Also, DBC‐RD had a smaller Eb value of 0.24 eV compared with that of TPE‐RD (0.42 eV). However, these molecules showed similar Eb values under dispersed conditions, which suggested that the decreased Eb of DBC‐RD in pristine film is induced by molecular aggregation. By comparison with TPE‐RD, DBC‐RD showed superior performances in single‐component organic solar cells and organic photocatalysts. These results indicate that a molecular design suitable for aggregation is important to decrease the Eb in films.

A Dibenzo[g,p]chrysene-Based Organic Semiconductor with Small Exciton Binding Energy via Molecular Aggregation.

Exciton binding energy (Eb) is understood as the energy required to dissociate an exciton in free-charge carriers, and is known to be an important parameter in determining the performance of organic opto-electronic devices. However, the development of a molecular design to achieve a small level of Eb in the solid state continues to lag behind. Here, to investigate the relationship between aggregation and Eb, star-shaped π-conjugated compounds DBC-RD and TPE-RD were developed using dibenzo[g,p]chrysene (DBC) and tetraphenylethylene (TPE). Theoretical calculations and physical measurements in solution showed no apparent differences between DBC-RD and TPE-RD, indicating that these molecules possess similar properties on a single-molecule level. By contrast, pristine films incorporating these molecules showed significantly different levels of electron affinity, ionization potential, and optical gap. Also, DBC-RD had a smaller Eb value of 0.24 eV compared with that of TPE-RD (0.42 eV). However, these molecules showed similar Eb values under dispersed conditions, which suggested that the decreased Eb of DBC-RD in pristine film is induced by molecular aggregation. By comparison with TPE-RD, DBC-RD showed superior performances in single-component organic solar cells and organic photocatalysts. These results indicate that a molecular design suitable for aggregation is important to decrease the Eb in films.

SigAlign: an alignment algorithm guided by explicit similarity criteria.

In biological sequence alignment, prevailing heuristic aligners achieve high-throughput by several approximation techniques, but at the cost of sacrificing the clarity of output criteria and creating complex parameter spaces. To surmount these challenges, we introduce 'SigAlign', a novel alignment algorithm that employs two explicit cutoffs for the results: minimum length and maximum penalty per length, alongside three affine gap penalties. Comparative analyses of SigAlign against leading database search tools (BLASTn, MMseqs2) and read mappers (BWA-MEM, bowtie2, HISAT2, minimap2) highlight its performance in read mapping and database searches. Our research demonstrates that SigAlign not only provides high sensitivity with a non-heuristic approach, but also surpasses the throughput of existing heuristic aligners, particularly for high-accuracy reads or genomes with few repetitive regions. As an open-source library, SigAlign is poised to become a foundational component to provide a transparent and customizable alignment process to new analytical algorithms, toolsand pipelines in bioinformatics.

Step-by-step design of new phenyl-1,2,3-triazole derivatives with improved anti-corrosive properties: A combined DFT and MD simulation study

In this study, 35 new inhibitors were designed theoretically through the step-by-step strategy based on a new organic non-planar inhibitor 1-benzyl-4-phenyl-1H-1,2,3-triazole (BPT). The first step is to replace one parent phenyl group by six other groups (–Cl, –Br, –OH, –NH2, –OCH3, –thiazole) with heteroatoms, trying to add the adsorption sites and reduce the energy gap. The second step is to use two bridge groups (–S–, –NH–) to displace the original bridge group (–CH2), or to delete the bridge group directly, tending to further add the adsorption sites, reduce the energy gap and change BPT to planar molecules. The final step is to use the combination of oxa and carbonylation substitution strategy on the six compounds with lowest energy gap obtained from the previous two step modifications, in order to further add the adsorption sites, reduce the energy gap and change BPT to planar molecules. Based on the quantum chemical calculations, it is found that main key parameters to anti-corrosive properties like the softness, electron affinity and energy gap were improved greatly compared to BPT. Three new planar molecules (E5, E6 and E6) which have high chemical reactivity, high binding energy with metals, and low energy gap were found successfully, which may be attractive potential inhibitors used as the corrosion inhibition to Fe-related alloy. The corrosion inhibition mechanism of E5 to E7 is different to that of BPT, in which the whole structure will make contributions to the interaction with metals to increase the binding energy and the corrosion inhibition efficiency. This work may provide a unique view for the design and development of new advanced inhibitor.

Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment Including Long Indels.

Despite having important biological implications, insertion, and deletion (indel) events are often disregarded or mishandled during phylogenetic inference. In multiple sequence alignment, indels are represented as gaps and are estimated without considering the distinct evolutionary history of insertions and deletions. Consequently, indels are usually excluded from subsequent inference steps, such as ancestral sequence reconstruction and phylogenetic tree search. Here, we introduce indel-aware parsimony (indelMaP), a novel way to treat gaps under the parsimony criterion by considering insertions and deletions as separate evolutionary events and accounting for long indels. By identifying the precise location of an evolutionary event on the tree, we can separate overlapping indel events and use affine gap penalties for long indel modeling. Our indel-aware approach harnesses the phylogenetic signal from indels, including them into all inference stages. Validation and comparison to state-of-the-art inference tools on simulated data show that indelMaP is most suitable for densely sampled datasets with closely to moderately related sequences, where it can reach alignment quality comparable to probabilistic methods and accurately infer ancestral sequences, including indel patterns. Due to its remarkable speed, our method is well suited for epidemiological datasets, eliminating the need for downsampling and enabling the exploitation of the additional information provided by dense taxonomic sampling. Moreover, indelMaP offers new insights into the indel patterns of biologically significant sequences and advances our understanding of genetic variability by considering gaps as crucial evolutionary signals rather than mere artefacts.

Affinity gaps among B cells in germinal centers drive the selection of MPER precursors

Current prophylactic human immunodeficiency virus 1 (HIV-1) vaccine research aims to elicit broadly neutralizing antibodies (bnAbs). Membrane-proximal external region (MPER)-targeting bnAbs, such as 10E8, provide exceptionally broad neutralization, but some are autoreactive. Here, we generated humanized B cell antigen receptor knock-in mouse models to test whether a series of germline-targeting immunogens could drive MPER-specific precursors toward bnAbs. We found that recruitment of 10E8 precursors to germinal centers (GCs) required a minimum affinity for germline-targeting immunogens, but the GC residency of MPER precursors was brief due to displacement by higher-affinity endogenous B cell competitors. Higher-affinity germline-targeting immunogens extended the GC residency of MPER precursors, but robust long-term GC residency and maturation were only observed for MPER-HuGL18, an MPER precursor clonotype able to close the affinity gap with endogenous B cell competitors in the GC. Thus, germline-targeting immunogens could induce MPER-targeting antibodies, and B cell residency in the GC may be regulated by a precursor–competitor affinity gap.

Band alignment studies of Zn1-xNixO/ZnO: As bilayer electron transport layer in perovskite solar cells

An efficient electron transport layer (ETL) is an essential requirement for performance and stability for perovskite solar cells. In this study, we have opted Zn1-xNixO/ZnO bilayer as is used electron transport layer instead of the ZnO single layer to overcome the trap-assisted recombination and also to enhance energy level alignment in the solar cell. For this, pristine ZnO and Ni-doped ZnO (Ni–ZnO) thin films were deposited on fused silica (Quartz) by pulsed laser deposition (PLD). For confirmation of the structural properties of deposited thin films, X-ray diffraction has been used. Electron affinity and band gap of these films have been evaluated by UPS and UV–Vis spectroscopy to design Zn1-xNixO/ZnO bilayer ETL. Further, planar perovskite solar cell has been schematized and simulated using SCAPS-1D software using experimentally designed bilayer ETL.

Vcfdist: accurately benchmarking phased small variant calls in human genomes

Accurately benchmarking small variant calling accuracy is critical for the continued improvement of human whole genome sequencing. In this work, we show that current variant calling evaluations are biased towards certain variant representations and may misrepresent the relative performance of different variant calling pipelines. We propose solutions, first exploring the affine gap parameter design space for complex variant representation and suggesting a standard. Next, we present our tool vcfdist and demonstrate the importance of enforcing local phasing for evaluation accuracy. We then introduce the notion of partial credit for mostly-correct calls and present an algorithm for clustering dependent variants. Lastly, we motivate using alignment distance metrics to supplement precision-recall curves for understanding variant calling performance. We evaluate the performance of 64 phased Truth Challenge V2 submissions and show that vcfdist improves measured insertion and deletion performance consistency across variant representations from R2 = 0.97243 for baseline vcfeval to 0.99996 for vcfdist.

Molecular Orbital Properties and Insulation Characteristics of Flaxseed Oil

This study aims to analyze the molecular orbital parameters of flaxseed oil (linum usitatissimum) and to measure the AC breakdown voltages at different electrode gaps with various rate of rises. AC breakdown voltages of flaxseed oil are measured at 1.0 and 2.5 mm electrode settings with 0.5 kV/s, 2.0 kV/s and 3.0 kV/s rate of rises, adhering to IEC and IEEE standards. UV-VIS (Ultraviolet–Visible) and FT-IR (Fourier Transform-Infrared) measurement tests carried out after breakdown voltage measurements reveals that the molecular structure of the oil remains stable against electrical discharges. The compounds of flaxseed oil are analyzed using GC-MS and it is determined that the oil mainly consists of seven triglycerides in accordance with the literature. In order to better understand the electrical behavior of these triglycerides, molecular orbital properties such as ionization potential, electron affinity and electron energy gap are analyzed employing Density Functional Theory (DFT) using B3LYP/6-311 + G(d,p) and B3PW91/6-311 + G(d,p) basis sets. The advantages of flaxseed oil such as AC dielectric strength, stability against breakdown mechanism, homogeneous molecular electrical characteristics of its compounds and antioxidant content make this oil as one of the potential natural ester alternatives to mineral oils in the power system industry.

Atom-Based Machine Learning Model for Quantitative Property-Structure Relationship of Electronic Properties of Fusenes and Substituted Fusenes.

This study presents the development of machine-learning-based quantitative structure-property relationship (QSPR) models for predicting electron affinity, ionization potential, and band gap of fusenes from different chemical classes. Three variants of the atom-based Weisfeiler-Lehman (WL) graph kernel method and the machine learning model Gaussian process regressor (GPR) were used. The data pool comprises polycyclic aromatic hydrocarbons (PAHs), thienoacenes, cyano-substituted PAHs, and nitro-substituted PAHs computed with density functional theory (DFT) at the B3LYP-D3/6-31+G(d) level of theory. The results demonstrate that the GPR/WL kernel methods can accurately predict the electronic properties of PAHs and their derivatives with root-mean-square deviations of 0.15 eV. Additionally, we also demonstrate the effectiveness of the active learning protocol for the GPR/WL kernel methods pipeline, particularly for data sets with greater diversity. The interpretation of the model for contributions of individual atoms to the predicted electronic properties provides reasons for the success of our previous degree of π-orbital overlap model.

Threshold Photoionization and Density Functional Theory Investigations of Small Lanthanum Monoxide Clusters, LanO (n = 2-10).

Small lanthanum monoxide clusters, LanO (n = 2-10), have been studied by laser threshold photoionization (PI) spectroscopy and density functional theory (DFT). Ionization energies (IEs) gradually decrease with cluster size with oscillatory behavior at certain sizes at n = 4, 7, and 9, and the IEs are slightly lower than the corresponding bare Lan clusters. Mulliken charge analysis of the neutral and cation clusters indicates that the threshold PI occurs from a delocalized metal-based 5d orbital. The stable geometric structures and IEs for the LanO (n = 2-8) clusters have been determined from DFT. Zero electron kinetic energy and PI spectra have been calculated based on DFT calculations and compared with the experimental PI spectra. On the basis of favorable agreement between the simulated and experimental PI spectra, reliable ground-state geometric structures have been assigned. The O atom is negatively charged, equivalent to one electronic charge mainly transferred from La atoms bonded to it. Chemical bonding between the La and O atoms is ionic, whereas La atoms are mostly covalently bonded. No direct correlation is found between the electronic properties like the IE, electron affinity, and HOMO-LUMO gap and the stability of these clusters.

Concurrent Design of Alloy Compositions of CZTSSe and CdZnS Using SCAPS Simulation: Potential Routes to Overcoming VOC Deficit

Solar energy is the most used renewable energy source. CZTSSe uses earth-abundant elements and has promising optoelectronic properties, resulting in becoming a viable alternative to thin film PV. This work provides design guidelines for CZTSSe-based solar cells, where CZTSSe has a tunable affinity and energy gap. The analysis is based on incorporating a ternary compound material to serve as an electron transport material (ETM). In this regard, CdZnS is a potential candidate that can be utilized as an electron transport layer whose affinity and energy gap can be tuned to adjust the band alignment at the ETL/CZTSSe interface. In order to design a high-efficiency solar cell, one has to tune both the ETL and absorber layers to have a suitable conduction band offset (CBO), thereby minimizing the non-radiative recombination which, in turn, boosts the power conversion efficiency (PCE). Thus, in our presented simulation study, we provide a codesign of alloy compositions of both the CZTSSe photoactive layer and the CdZnS ETL using SCAPS-1D simulation. It is found that using the codesign of alloy compositions of the ternary compound ETL and the absorber enhances the PCE by about 2% and, more importantly, overcomes the main issue in CZTSSe which is its open-circuit voltage (VOC) deficit. Furthermore, upon optimizing the thickness and doping of both the ETL and absorber layer, as well as the bulk defect of the absorber layer, a PCE of 17.16% is attained in this study, while the calibrated PCE based on a previously published experimental work was 12.30%.

Structural optimization of inverted CsPbI2Br perovskite solar cells for enhanced performance via SCAPS-1D simulation

The CsPbI2Br material benefits perovskite solar cells (PSCs) by balancing their efficiency with chemical and thermal stability. Herein, we performed numerical modeling of a p-i-n structured PSCs employing different electron transport layers (ETLs). In order to optimize the ETL, the simulation results showed bilayer ETL (PCBM/SnO2) yielded the best device performance. Then, by tweaking the absorber layer’s defect density, thickness, electron affinity, and band gap, we optimized the device performance utilizing this bilayer ETL and yielded power conversion efficiency (PCE) of 12.51%, fill factor (FF) of 73.60%, open circuit voltage (V OC ) of 0.94 V, and short circuit current density (J SC ) of 17.94 mA cm−2. These CsPbI2Br perovskite-based devices would have outstanding thermal stability in a range from 253 K to 323 K. Another important observation in these PSCs is that interfacial defect density plays a crucial for regulating the V OC. We, therefore, anticipate that this research will aid in the development of extremely effective and stable inverted all inorganic PSCs.

Chemical Adsorption of HF, HCl, and H2O onto YF3 and Isostructural HoF3 Surfaces by First Principles

The two elements, yttrium and holmium, form a geochemical twin pair as their cations possess equivalent ratios of charge to radius. However, despite their equal electrostatics, a subtle difference in their fluoride or chloride affinity is known within solutions. In this work, we investigated whether this affinity gap is also present within the solid phase and how it depends on the surface configuration. We modeled adsorptions onto β-YF3 (waimirite) and isostructural β-HoF3 by periodic density functional theory. To draw conclusions on the affinity toward fluoride and chloride vs. water, adsorbates of HF, HCl, or H2O onto any of the four highly abundant surfaces of (010), (100), (011), and (101) were studied. Among others, the conformational landscape was explored by 200 ps of ab initio molecular dynamics. For stoichiometric surfaces of both MF3, we indeed found stronger adsorptions for HF than HCl. All (hkl)·H2O showed slightly stronger adsorption energies for HoF3, while for HF and HCl, the metal preferences varied by the surface. While (100) showed the strongest preference for HoF3, (101) preferred YF3 by the same magnitude.

NPoRe: n-polymer realigner for improved pileup-based variant calling

Despite recent improvements in nanopore basecalling accuracy, germline variant calling of small insertions and deletions (INDELs) remains poor. Although precision and recall for single nucleotide polymorphisms (SNPs) now exceeds 99.5%, INDEL recall remains below 80% for standard R9.4.1 flow cells. We show that read phasing and realignment can recover a significant portion of false negative INDELs. In particular, we extend Needleman-Wunsch affine gap alignment by introducing new gap penalties for more accurately aligning repeated n-polymer sequences such as homopolymers (n=1) and tandem repeats (2 le n le 6). At the same precision, haplotype phasing improves INDEL recall from 63.76 to 70.66% and nPoRe realignment improves it further to 73.04%.

Semi-Empirical Investigation of Electronic, Vibrational and Thermodynamic Properties of Perylene Molecule (C20H12)

This work investigates computationally the spectroscopic and thermodynamics properties of the perylene molecule (C20H12) in the gas phase by utilizing a semi-empirical method [Hyper Chem8.0 and WinMopac7.0] programs, via (MNDO-PM3). This method is providing more simplicity and quick performance. The electronic properties such as total energy, dissociation energy, molecular orbital, ionization potentials, electronic affinity, and energy gap were calculated. However, vibration analysis and UV-visible spectra have been calculated. Moreover, the thermodynamic properties at the standard temperature such as heat of formation, entropy, enthalpy, heat capacity, and Gibbs free energy were calculated.

BpRNA-align: improved RNA secondary structure global alignment for comparing and clustering RNA structures.

Ribonucleic acid (RNA) is a polymeric molecule that is fundamental to biological processes, with structure being more highly conserved than primary sequence and often key to its function. Advances in RNA structure characterization have resulted in an increase in the number of accurate secondary structures. The task of uncovering common RNA structural motifs with a collective function through structural comparison, providing a level of similarity, remains challenging and could be used to improve RNA secondary structure databases and discover new RNA families. In this work, we present a novel secondary structure alignment method, bpRNA-align. bpRNA-align is a customized global structural alignment method, utilizing an inverted (gap extend costs more than gap open) and context-specific affine gap penalty along with a structural, feature-specific substitution matrix to provide similarity scores. We evaluate our similarity scores in comparison to other methods, using affinity propagation clustering, applied to a benchmarking data set of known structure types. bpRNA-align shows improvement in clustering performance over a broad range of structure types.

Tailoring charge affinity, dielectric property, and band gap of bacterial cellulose paper by multifunctional Ti2NbO7 nanosheets for improving triboelectric nanogenerator performance

Tailoring charge affinity, dielectric property, and band gap of bacterial cellulose paper by multifunctional Ti2NbO7 nanosheets for improving triboelectric nanogenerator performance

Adsorption differences and mechanism of chitooligosaccharides with specific degree of polymerization on macroporous resins with different functional groups

Ion exchange resins are promising materials for separating chitooligosaccharides (COSs) with different degrees of polymerization (DP). The adsorbent functional groups significantly determine the interactions with COSs and affect their adsorption and separation efficiency. This study investigated the adsorption behaviors of COSs on macroporous cation exchange resins with different functional groups to clarify the functional group effect on the adsorption of COSs with different DP, which can also help to provide a theoretical basis for the selection of separation medium and optimization of the separation technics of COSs. The results showed that the adsorption of COSs on sulfonic-acid type resin DX-10 and carboxylic-acid type resin DC-10 were favorable, and the adsorption isotherms were in accord with the Sips model. Adsorption thermodynamics showed that temperature had opposite effects on the two resins' equilibrium adsorption capacity of COSs. The diffusion coefficient of COSs on DX-10 resin was greater, and the affinity gap between COSs on DX-10 resin was larger than that of DC-10 resin, which is beneficial for improving the separation resolution of COSs. In contrast, the interaction energy between COSs with high DP and DC-10 resin was weaker compared with DX-10, which made the elution of COSs with high DP easier.

Theoretical study of electronic and optical properties of functionalized Indigo and Alizarin as potential organic semi-conductors for solar cells applications

The optical and electronic properties of two conjugated organic molecules, Indigo and Alizarin, as potential organic solar cells were studied theoretically. The electronic properties, reorganization energy (λh and λe), adiabatic Ionization potential (IA), adiabatic Electron affinity (EA),HOMO, LUMO and Energy gap (Eg) were calculated using DFT. The optical properties as the maximum absorption (λmax) along with oscillator strengths (f) at the excited states in vacuum and solvent were also calculated using TD-DFT. The molecules were functionalized by electronegative functional groups to understand the effect of functionalization on the optical and electronic properties. It was found that the functionalization of Indigo and Alizarin has resulted in overall conversion of the materials to better n-type molecules. The Eg for both molecules has been generally reduced upon the introduction of electronegative functional groups. This indicates the possibility of tuning organic molecules optical and electronic properties by introducing functional groups. Also, both studied molecules along with their functionalized molecules show properties that fall among organic semiconductors and thereby, can be potentially used in solar cells.